Takuji Yamada

According to our database, Takuji Yamada authored at least 15 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

QNetDiff: a quantitative measurement of network rewiring.

Shota Nose, Hirotsugu Shiroma, Takuji Yamada, Yushi Uno

BMC Bioinform., December, 2024

2019

FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization.

Youssef Darzi, Yuta Yamate, Takuji Yamada

Bioinform., 2019

2018

iPath3.0: interactive pathways explorer v3.

Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada

Nucleic Acids Res., 2018

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.

Hiroshi Mori, Takayuki Maruyama, Masahiro Yano, Takuji Yamada, Ken Kurokawa

BMC Syst. Biol., 2018

2016

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

Yuki Moriya, Takuji Yamada, Shujiro Okuda, Zenichi Nakagawa, Masaaki Kotera, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto

J. Chem. Inf. Model., 2016

2015

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.

Tianmin Wang, Hiroshi Mori, Chong Zhang, Ken Kurokawa, Xin-Hui Xing, Takuji Yamada

BMC Bioinform., 2015

2014

Addendum: Enterotypes of the human gut microbiome.

Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Brüls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernández, Laurent Gautier, Torben Hansen, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, Henrik Bjørn Nielsen, Trine Rask Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Pontén, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang, Francisco Guarner, Oluf Pedersen, Willem M. de Vos, Søren Brunak, Joël Dore, MetaHIT consortium, Jean Weissenbach, S. Dusko Ehrlich, Peer Bork

Nat., 2014

CLAST: CUDA implemented large-scale alignment search tool.

Masahiro Yano, Hiroshi Mori, Yutaka Akiyama, Takuji Yamada, Ken Kurokawa

BMC Bioinform., 2014

2011

iPath2.0: interactive pathway explorer.

Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, Peer Bork

Nucleic Acids Res., 2011

2008

KEGG Atlas mapping for global analysis of metabolic pathways.

Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, Minoru Kanehisa

Nucleic Acids Res., 2008

2007

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi

Nucleic Acids Res., 2007

Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways.

Mina Oh, Takuji Yamada, Masahiro Hattori, Susumu Goto, Minoru Kanehisa

J. Chem. Inf. Model., 2007

2006

Extraction of phylogenetic network modules from the metabolic network.

Takuji Yamada, Minoru Kanehisa, Susumu Goto

BMC Bioinform., 2006

2005

VisANT: data-integrating visual framework for biological networks and modules.

Zhenjun Hu, Joe Mellor, Jie Wu, Takuji Yamada, Dustin T. Holloway, Charles DeLisi

Nucleic Acids Res., 2005

2004

Clustering under the line graph transformation: application to reaction network.

Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu

BMC Bioinform., 2004